use of cbit.vcell.biomodel.meta.MiriamManager in project vcell by virtualcell.
the class MiriamTreeModel method createTree.
public void createTree(Identifiable identifiable) {
if (identifiable == null) {
((DefaultMutableTreeNode) getRoot()).removeAllChildren();
fireTreeStructureChanged(this, getPathToRoot(((DefaultMutableTreeNode) getRoot())), null, null);
return;
}
((DefaultMutableTreeNode) getRoot()).removeAllChildren();
MiriamManager miriamManager = vcMetaData.getMiriamManager();
TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>> miriamDescrHeir = miriamManager.getMiriamTreeMap();
Map<MiriamRefGroup, MIRIAMQualifier> refGroupMap = miriamDescrHeir.get(identifiable);
VCID vcid = vcMetaData.getIdentifiableProvider().getVCID(identifiable);
// Map<Identifiable, Map<DateQualifier, Set<DublinCoreDate>>> dateMapMap = miriamManager.getDublinCoreDateMap();
// Map<DateQualifier, Set<DublinCoreDate>> dateMap = dateMapMap.get(identifiable);
List<LinkNode> nodeList = new ArrayList<>();
if (refGroupMap != null) {
for (MiriamRefGroup refGroup : refGroupMap.keySet()) {
MIRIAMQualifier qualifier = refGroupMap.get(refGroup);
for (MiriamResource miriamResource : refGroup.getMiriamRefs()) {
LinkNode ln = new LinkNode(qualifier, miriamResource);
nodeList.add(ln);
}
}
Collections.sort(nodeList);
for (LinkNode ln : nodeList) {
((DefaultMutableTreeNode) getRoot()).add(ln);
}
}
// if (dateMap!=null){
// for (DublinCoreQualifier.DateQualifier qualifier : dateMap.keySet()){
// Set<DublinCoreDate> dates = dateMap.get(qualifier);
// for (DublinCoreDate date : dates){
// ((DefaultMutableTreeNode)getRoot()).add(new DateNode(qualifier,date));
// }
// }
// }
fireTreeStructureChanged(this, getPathToRoot(((DefaultMutableTreeNode) getRoot())), null, null);
}
use of cbit.vcell.biomodel.meta.MiriamManager in project vcell by virtualcell.
the class SpeciesContextShape method paintSelf.
@Override
public void paintSelf(Graphics2D g, int absPosX, int absPosY) {
boolean isBound = false;
SpeciesContext sc = (SpeciesContext) getModelObject();
boolean bHasPCLink = false;
if (graphModel instanceof ModelCartoon) {
ModelCartoon mc = (ModelCartoon) graphModel;
// check if species has Pathway Commons link by querying VCMetadata : if it does, need to change color of speciesContext.
try {
MiriamManager miriamManager = mc.getModel().getVcMetaData().getMiriamManager();
Map<MiriamRefGroup, MIRIAMQualifier> miriamRefGroups = miriamManager.getAllMiriamRefGroups(sc.getSpecies());
if (miriamRefGroups != null && miriamRefGroups.size() > 0) {
bHasPCLink = true;
}
} catch (Exception e) {
e.printStackTrace(System.out);
}
}
if (sc.getSpecies().getDBSpecies() != null || bHasPCLink) {
isBound = true;
}
int shapeHeight = getSpaceManager().getSize().height;
int shapeWidth = getSpaceManager().getSize().width;
int offsetX = (shapeWidth - circleDiameter) / 2;
int offsetY = (shapeHeight - circleDiameter) / 2;
Graphics2D g2D = g;
// if (icon == null) {
icon = new Area();
icon.add(new Area(new Ellipse2D.Double(offsetX, offsetY, circleDiameter, circleDiameter)));
// icon.add(new Area(new RoundRectangle2D.Double(offsetX, offsetY,circleDiameter,circleDiameter,circleDiameter/2,circleDiameter/2)));
// }
Area movedIcon = icon.createTransformedArea(AffineTransform.getTranslateInstance(absPosX, absPosY));
if (sc.getSpeciesPattern() == null) {
defaultBG = java.awt.Color.green;
} else {
defaultBG = java.awt.Color.blue;
}
if (isCatalyst == true) {
defaultBG = java.awt.Color.magenta;
}
backgroundColor = defaultBG;
darkerBackground = backgroundColor.darker().darker();
// g.setColor((!isBound && !isSelected()?darkerBackground:backgroundColor));
g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
Color exterior = !isBound && !isSelected() ? darkerBackground : backgroundColor;
// Color interior = exterior.brighter().brighter();
Point2D center = new Point2D.Float(absPosX + circleDiameter * 0.5f, absPosY + circleDiameter * 0.5f);
float radius = circleDiameter * 0.5f;
Point2D focus = new Point2D.Float(absPosX + circleDiameter * 0.4f, absPosY + circleDiameter * 0.4f);
float[] dist = { 0.1f, 1.0f };
Color[] colors = { Color.white, exterior };
// Color[] colors = {interior, exterior};
RadialGradientPaint p = new RadialGradientPaint(center, radius, focus, dist, colors, CycleMethod.NO_CYCLE);
g2D.setPaint(p);
g2D.fill(movedIcon);
g.setColor(forgroundColor);
g2D.draw(movedIcon);
// draw label
if (getLabel() != null && getLabel().length() > 0) {
if (isSelected()) {
// clear background and outline to make selected label stand out
Rectangle outlineRectangle = getLabelOutline(absPosX, absPosY);
drawRaisedOutline(outlineRectangle.x, outlineRectangle.y, outlineRectangle.width, outlineRectangle.height, g, Color.white, forgroundColor, Color.gray);
}
g.setColor(forgroundColor);
g.drawString((isSelected() || smallLabel == null ? getLabel() : smallLabel), (isSelected() || smallLabel == null ? getLabelPos().x : smallLabelPos.x) + absPosX, getLabelPos().y + absPosY);
}
if (linkText != null && linkText != "") {
ShapePaintUtil.paintLinkMark(g2D, this, Color.BLACK);
}
}
use of cbit.vcell.biomodel.meta.MiriamManager in project vcell by virtualcell.
the class BioModelEditorModelPanel method initialize.
private void initialize() {
newButton = new JButton("New");
newButton2 = new JButton("New Rule");
newMemButton = new JButton("New Membrane");
deleteButton = new JButton("Delete");
duplicateButton = new JButton("Duplicate");
pathwayButton = new JButton("Pathway Links", new DownArrowIcon());
pathwayButton.setHorizontalTextPosition(SwingConstants.LEFT);
textFieldSearch = new JTextField();
textFieldSearch.putClientProperty("JTextField.variant", "search");
structuresTable = new EditorScrollTable();
reactionsTable = new EditorScrollTable();
speciesTable = new EditorScrollTable();
molecularTypeTable = new EditorScrollTable();
observablesTable = new EditorScrollTable();
structureTableModel = new BioModelEditorStructureTableModel(structuresTable);
reactionTableModel = new BioModelEditorReactionTableModel(reactionsTable);
speciesTableModel = new BioModelEditorSpeciesTableModel(speciesTable);
molecularTypeTableModel = new MolecularTypeTableModel(molecularTypeTable);
observableTableModel = new ObservableTableModel(observablesTable);
structuresTable.setModel(structureTableModel);
reactionsTable.setModel(reactionTableModel);
speciesTable.setModel(speciesTableModel);
molecularTypeTable.setModel(molecularTypeTableModel);
observablesTable.setModel(observableTableModel);
reactionCartoonEditorPanel = new ReactionCartoonEditorPanel();
reactionCartoonEditorPanel.addPropertyChangeListener(eventHandler);
reactionCartoonEditorPanel.getReactionCartoonFull().addPropertyChangeListener(eventHandler);
reactionCartoonEditorPanel.getReactionCartoonMolecule().addPropertyChangeListener(eventHandler);
reactionCartoonEditorPanel.getReactionCartoonRule().addPropertyChangeListener(eventHandler);
// cartoonEditorPanel = new CartoonEditorPanelFixed();
// cartoonEditorPanel.getStructureCartoon().addPropertyChangeListener(eventHandler);
/* button panel */
buttonPanel = new JPanel();
buttonPanel.setLayout(new GridBagLayout());
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 0;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(newButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = 0;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(newButton2, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 2;
gbc.gridy = 0;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(newMemButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 3;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(duplicateButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 4;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(deleteButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 5;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(pathwayButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 6;
gbc.gridy = 0;
gbc.weightx = 0.5;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(4, 4, 4, 4);
buttonPanel.add(Box.createRigidArea(new Dimension(5, 5)), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 7;
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
gbc.insets = new Insets(4, 4, 4, 4);
buttonPanel.add(new JLabel("Search "), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 8;
gbc.gridy = 0;
gbc.weightx = 1.5;
gbc.anchor = GridBagConstraints.LINE_START;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(4, 4, 4, 4);
buttonPanel.add(textFieldSearch, gbc);
/* button panel */
tabbedPane = new JTabbedPaneEnhanced();
tabbedPane.setTabLayoutPolicy(JTabbedPane.SCROLL_TAB_LAYOUT);
modelPanelTabs[ModelPanelTabID.reaction_diagram.ordinal()] = new ModelPanelTab(ModelPanelTabID.reaction_diagram, reactionCartoonEditorPanel, VCellIcons.diagramIcon);
// modelPanelTabs[ModelPanelTabID.structure_diagram.ordinal()] = new ModelPanelTab(ModelPanelTabID.structure_diagram, cartoonEditorPanel, VCellIcons.structureIcon);
modelPanelTabs[ModelPanelTabID.reaction_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.reaction_table, reactionsTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.structure_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.structure_table, structuresTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.species_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.species_table, speciesTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.species_definitions_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.species_definitions_table, molecularTypeTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.observables_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.observables_table, observablesTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
tabbedPane.addChangeListener(eventHandler);
tabbedPane.addMouseListener(eventHandler);
for (ModelPanelTab tab : modelPanelTabs) {
tab.getComponent().setBorder(GuiConstants.TAB_PANEL_BORDER);
tabbedPane.addTab(tab.getName(), tab.getIcon(), tab.getComponent());
}
// tabbedPane.addChangeListener(changeListener);
setLayout(new BorderLayout());
add(tabbedPane, BorderLayout.CENTER);
add(buttonPanel, BorderLayout.SOUTH);
newButton.addActionListener(eventHandler);
newButton2.addActionListener(eventHandler);
newMemButton.addActionListener(eventHandler);
duplicateButton.addActionListener(eventHandler);
duplicateButton.setEnabled(false);
deleteButton.addActionListener(eventHandler);
deleteButton.setEnabled(false);
pathwayButton.addActionListener(eventHandler);
pathwayButton.setEnabled(false);
textFieldSearch.addActionListener(eventHandler);
textFieldSearch.getDocument().addDocumentListener(eventHandler);
structuresTable.getSelectionModel().addListSelectionListener(eventHandler);
reactionsTable.getSelectionModel().addListSelectionListener(eventHandler);
speciesTable.getSelectionModel().addListSelectionListener(eventHandler);
molecularTypeTable.getSelectionModel().addListSelectionListener(eventHandler);
observablesTable.getSelectionModel().addListSelectionListener(eventHandler);
DefaultScrollTableCellRenderer tableRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (value instanceof Structure) {
setText(((Structure) value).getName());
} else if (value instanceof Kinetics) {
setText(((Kinetics) value).getKineticsDescription().getDescription());
} else if (value instanceof RbmKineticLaw) {
setText(((RbmKineticLaw) value).getRateLawType().name());
}
return this;
}
};
RbmTableRenderer rbmTableRenderer = new RbmTableRenderer();
structuresTable.setDefaultRenderer(Structure.class, tableRenderer);
speciesTable.setDefaultRenderer(Structure.class, tableRenderer);
reactionsTable.setDefaultRenderer(Structure.class, tableRenderer);
reactionsTable.setDefaultRenderer(Kinetics.class, tableRenderer);
reactionsTable.setDefaultRenderer(RbmKineticLaw.class, tableRenderer);
reactionsTable.setDefaultRenderer(ModelProcessDynamics.class, tableRenderer);
// Link to biopax object Table Cell Renderer
DefaultScrollTableCellRenderer linkTableCellRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
BioModelEntityObject bioModelEntityObject = null;
if (table.getModel() instanceof VCellSortTableModel<?>) {
if (table.getModel() == reactionTableModel && reactionTableModel.getValueAt(row) instanceof BioModelEntityObject) {
bioModelEntityObject = (BioModelEntityObject) reactionTableModel.getValueAt(row);
} else if (table.getModel() == speciesTableModel) {
bioModelEntityObject = speciesTableModel.getValueAt(row);
} else if (table.getModel() == molecularTypeTableModel) {
bioModelEntityObject = molecularTypeTableModel.getValueAt(row);
}
if (bioModelEntityObject != null) {
Set<RelationshipObject> relationshipSet = bioModel.getRelationshipModel().getRelationshipObjects(bioModelEntityObject);
if (relationshipSet.size() > 0) {
StringBuilder tooltip = new StringBuilder("<html>Links to Pathway objects:<br>");
for (RelationshipObject ro : relationshipSet) {
tooltip.append("<li>" + ro.getBioPaxObject() + "</li>");
}
if (!isSelected) {
setForeground(Color.blue);
}
String finalName = null;
BioPaxObject bioPaxObject = relationshipSet.iterator().next().getBioPaxObject();
if (bioPaxObject instanceof EntityImpl && ((EntityImpl) bioPaxObject).getName() != null && ((EntityImpl) bioPaxObject).getName().size() > 0) {
finalName = ((EntityImpl) bioPaxObject).getName().get(0);
} else if (bioPaxObject instanceof Conversion) {
Conversion mp = (Conversion) bioPaxObject;
finalName = "[" + bioPaxObject.getIDShort() + "]";
} else {
finalName = bioModelEntityObject.getName();
}
final int LIMIT = 40;
final String DOTS = "...";
if (finalName != null && finalName.length() > LIMIT) {
finalName = finalName.substring(0, LIMIT - DOTS.length() - 1) + DOTS;
}
setText("<html><u>" + finalName + "</u></html>");
setToolTipText(tooltip.toString());
}
}
}
return this;
}
};
// Annotations icon column renderer
DefaultScrollTableCellRenderer annotationTableCellRenderer = new DefaultScrollTableCellRenderer() {
final Color lightBlueBackground = new Color(214, 234, 248);
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
Identifiable entity = null;
if (table.getModel() instanceof VCellSortTableModel<?>) {
if (table.getModel() == reactionTableModel) {
entity = (BioModelEntityObject) reactionTableModel.getValueAt(row);
} else if (table.getModel() == speciesTableModel) {
entity = speciesTableModel.getValueAt(row);
} else if (table.getModel() == molecularTypeTableModel) {
entity = molecularTypeTableModel.getValueAt(row);
} else if (table.getModel() == observableTableModel) {
entity = observableTableModel.getValueAt(row);
} else if (table.getModel() == structureTableModel) {
entity = structureTableModel.getValueAt(row);
}
if (entity != null) {
if (isSelected) {
setBackground(lightBlueBackground);
}
Identifiable identifiable = AnnotationsPanel.getIdentifiable(entity);
String freeText = bioModel.getVCMetaData().getFreeTextAnnotation(identifiable);
MiriamManager miriamManager = bioModel.getVCMetaData().getMiriamManager();
TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>> miriamDescrHeir = miriamManager.getMiriamTreeMap();
Map<MiriamRefGroup, MIRIAMQualifier> refGroupMap = miriamDescrHeir.get(identifiable);
Icon icon1 = VCellIcons.issueGoodIcon;
Icon icon2 = VCellIcons.issueGoodIcon;
if (freeText != null && !freeText.isEmpty()) {
icon2 = VCellIcons.noteIcon;
// icon = VCellIcons.bookmarkIcon;
// icon = VCellIcons.addIcon(icon, VCellIcons.linkIcon);
// icon = VCellIcons.addIcon(icon, VCellIcons.certificateIcon);
// icon = VCellIcons.addIcon(icon, VCellIcons.noteIcon);
}
if (refGroupMap != null && !refGroupMap.isEmpty()) {
icon1 = VCellIcons.linkIcon;
}
Icon icon = VCellIcons.addIcon(icon1, icon2);
setIcon(icon);
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmReactionExpressionCellRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == reactionTableModel) {
selectedObject = reactionTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof ReactionRule && value instanceof ModelProcessEquation) {
String text = "<html>";
text += "Reaction Rule";
text += "</html>";
setText(text);
} else {
// plain reaction, check if reactants have species pattern
ReactionStep rs = (ReactionStep) selectedObject;
String text = "<html>";
for (int i = 0; i < rs.getNumReactants(); i++) {
Reactant p = rs.getReactant(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
// text += "<b>" + p.getName() + "</b>";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumReactants() - 1) {
text += " + ";
}
}
text += " -> ";
for (int i = 0; i < rs.getNumProducts(); i++) {
Product p = rs.getProduct(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
// text += "<b>" + p.getName() + "</b>";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumProducts() - 1) {
text += " + ";
}
}
text += "</html>";
setText(text);
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmReactionDefinitionCellRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == reactionTableModel) {
selectedObject = reactionTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof ReactionRule && value instanceof ModelProcessEquation) {
ReactionRule rr = (ReactionRule) selectedObject;
String text = "<html>";
for (int i = 0; i < rr.getReactantPatterns().size(); i++) {
ReactantPattern rp = rr.getReactantPattern(i);
if (rp.getStructure() != null && !rp.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
text += "@" + rp.getStructure().getName() + ":";
}
text += RbmUtils.toBnglString(rp.getSpeciesPattern(), null, CompartmentMode.hide, 0);
// text += RbmTableRenderer.toHtml(rp.getSpeciesPattern(), isSelected);
if (i < rr.getReactantPatterns().size() - 1) {
text += "+";
}
}
if (rr.isReversible()) {
// <-> <->
text += " <-> ";
} else {
text += " -> ";
}
for (int i = 0; i < rr.getProductPatterns().size(); i++) {
ProductPattern pp = rr.getProductPattern(i);
if (pp.getStructure() != null && !pp.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
text += "@" + pp.getStructure().getName() + ":";
}
text += RbmUtils.toBnglString(pp.getSpeciesPattern(), null, CompartmentMode.hide, 0);
if (i < rr.getProductPatterns().size() - 1) {
text += "+";
}
}
text += "</html>";
setText(text);
} else {
// plain reaction, check if reactants have species pattern
ReactionStep rs = (ReactionStep) selectedObject;
String text = "<html>";
for (int i = 0; i < rs.getNumReactants(); i++) {
Reactant p = rs.getReactant(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumReactants() - 1) {
text += " + ";
}
}
if (rs.isReversible()) {
// <-> <->
text += " <-> ";
} else {
text += " -> ";
}
for (int i = 0; i < rs.getNumProducts(); i++) {
Product p = rs.getProduct(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumProducts() - 1) {
text += " + ";
}
}
text += "</html>";
setText(text);
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmObservablePatternCellRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == observableTableModel) {
selectedObject = observableTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof RbmObservable && value instanceof String) {
RbmObservable o = (RbmObservable) selectedObject;
String text = "<html>";
for (int i = 0; i < o.getSpeciesPatternList().size(); i++) {
SpeciesPattern sp = o.getSpeciesPattern(i);
text += RbmTableRenderer.toHtml(sp, isSelected);
if (i < o.getSpeciesPatternList().size() - 1) {
text += " ";
}
}
text = RbmUtils.appendSequence(text, o);
text += "</html>";
setText(text);
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmSpeciesNameCellRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == speciesTableModel) {
selectedObject = speciesTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof SpeciesContext) {
SpeciesContext sc = (SpeciesContext) selectedObject;
String text = "<html>";
if (sc.hasSpeciesPattern()) {
text += "<b>" + sc.getName() + "</b>";
} else {
text += sc.getName();
}
text += "</html>";
setText(text);
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer reactionNameCellRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == reactionTableModel) {
selectedObject = reactionTableModel.getValueAt(row);
}
setToolTipText(null);
if (selectedObject != null) {
if (selectedObject instanceof ReactionStep) {
ReactionStep rs = (ReactionStep) selectedObject;
String sbmlName = rs.getSbmlName();
if (sbmlName != null && !sbmlName.isEmpty()) {
String text = "<html>";
text += sbmlName;
text += "</html>";
setToolTipText(text);
} else {
setToolTipText(rs.getDisplayName());
}
} else if (selectedObject instanceof ReactionRule) {
ReactionRule rr = (ReactionRule) selectedObject;
setToolTipText(rr.getDisplayName());
}
}
}
return this;
}
};
//
// this renderer only paints the molecular type small shape in the MolecularType Table
//
DefaultScrollTableCellRenderer rbmMolecularTypeShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {
MolecularTypeSmallShape stls = null;
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == molecularTypeTableModel) {
selectedObject = molecularTypeTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof MolecularType) {
MolecularType mt = (MolecularType) selectedObject;
Graphics cellContext = table.getGraphics();
if (mt != null) {
stls = new MolecularTypeSmallShape(4, 3, mt, null, cellContext, mt, null, issueManager);
}
}
} else {
stls = null;
}
}
return this;
}
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
if (stls != null) {
stls.paintSelf(g);
}
}
};
// painting of species patterns small shapes inside the species context table
DefaultScrollTableCellRenderer rbmSpeciesShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {
SpeciesPatternSmallShape spss = null;
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == speciesTableModel) {
selectedObject = speciesTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof SpeciesContext) {
SpeciesContext sc = (SpeciesContext) selectedObject;
// sp may be null for "plain" species contexts
SpeciesPattern sp = sc.getSpeciesPattern();
Graphics panelContext = table.getGraphics();
spss = new SpeciesPatternSmallShape(4, 2, sp, panelContext, sc, isSelected, issueManager);
}
} else {
spss = null;
}
}
setText("");
return this;
}
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
if (spss != null) {
spss.paintSelf(g);
}
}
};
// ---------------------------------------------------------------------------------------------------------------------------------
DefaultScrollTableCellRenderer rbmReactionShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {
List<SpeciesPatternSmallShape> spssList = new ArrayList<SpeciesPatternSmallShape>();
SpeciesPatternSmallShape spss = null;
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == reactionTableModel) {
selectedObject = reactionTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof ReactionRule) {
ReactionRule rr = (ReactionRule) selectedObject;
Graphics panelContext = table.getGraphics();
spssList.clear();
List<ReactantPattern> rpList = rr.getReactantPatterns();
int xPos = 4;
for (int i = 0; i < rpList.size(); i++) {
SpeciesPattern sp = rr.getReactantPattern(i).getSpeciesPattern();
spss = new SpeciesPatternSmallShape(xPos, 2, sp, null, panelContext, rr, isSelected, issueManager);
if (i < rpList.size() - 1) {
spss.addEndText("+");
} else {
if (rr.isReversible()) {
spss.addEndText("<->");
xPos += 7;
} else {
spss.addEndText("->");
}
}
xPos += spss.getWidth() + 15;
spssList.add(spss);
}
List<ProductPattern> ppList = rr.getProductPatterns();
xPos += 7;
for (int i = 0; i < ppList.size(); i++) {
SpeciesPattern sp = rr.getProductPattern(i).getSpeciesPattern();
spss = new SpeciesPatternSmallShape(xPos, 2, sp, null, panelContext, rr, isSelected, issueManager);
if (i < ppList.size() - 1) {
spss.addEndText("+");
}
xPos += spss.getWidth() + 15;
spssList.add(spss);
}
} else {
ReactionStep rs = (ReactionStep) selectedObject;
Graphics panelContext = table.getGraphics();
spssList.clear();
int xPos = 4;
int extraSpace = 0;
for (int i = 0; i < rs.getNumReactants(); i++) {
SpeciesPattern sp = rs.getReactant(i).getSpeciesContext().getSpeciesPattern();
spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, rs, isSelected, issueManager);
if (i < rs.getNumReactants() - 1) {
spss.addEndText("+");
} else {
if (rs.isReversible()) {
spss.addEndText("<->");
extraSpace += 7;
} else {
spss.addEndText("->");
}
}
int offset = sp == null ? 17 : 15;
offset += extraSpace;
int w = spss.getWidth();
xPos += w + offset;
spssList.add(spss);
}
xPos += 8;
for (int i = 0; i < rs.getNumProducts(); i++) {
SpeciesPattern sp = rs.getProduct(i).getSpeciesContext().getSpeciesPattern();
if (i == 0 && rs.getNumReactants() == 0) {
xPos += 14;
}
spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, rs, isSelected, issueManager);
if (i == 0 && rs.getNumReactants() == 0) {
spss.addStartText("->");
}
if (i < rs.getNumProducts() - 1) {
spss.addEndText("+");
}
int offset = sp == null ? 17 : 15;
int w = spss.getWidth();
xPos += w + offset;
spssList.add(spss);
}
}
} else {
spssList.clear();
}
}
setText("");
return this;
}
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
for (SpeciesPatternSmallShape spss : spssList) {
if (spss == null) {
continue;
}
spss.paintSelf(g);
}
}
};
// -------------------------------------------------------------------------------------------------------------------------------
DefaultScrollTableCellRenderer rbmObservableShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {
List<SpeciesPatternSmallShape> spssList = new ArrayList<SpeciesPatternSmallShape>();
SpeciesPatternSmallShape spss = null;
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == observableTableModel) {
selectedObject = observableTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof RbmObservable) {
RbmObservable observable = (RbmObservable) selectedObject;
Graphics panelContext = table.getGraphics();
int xPos = 4;
spssList.clear();
for (int i = 0; i < observable.getSpeciesPatternList().size(); i++) {
SpeciesPattern sp = observable.getSpeciesPatternList().get(i);
spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, observable, isSelected, issueManager);
xPos += spss.getWidth() + 6;
spssList.add(spss);
}
}
} else {
spssList.clear();
}
}
setText("");
return this;
}
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
for (SpeciesPatternSmallShape spss : spssList) {
if (spss == null) {
continue;
}
spss.paintSelf(g);
}
}
};
// TODO: here are the renderers associated with the columns
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_NAME).setCellRenderer(reactionNameCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_LINK).setCellRenderer(linkTableCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_EQUATION).setCellRenderer(rbmReactionExpressionCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEFINITION).setCellRenderer(rbmReactionDefinitionCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_NOTES).setCellRenderer(annotationTableCellRenderer);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NAME).setCellRenderer(rbmSpeciesNameCellRenderer);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_LINK).setCellRenderer(linkTableCellRenderer);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NOTES).setCellRenderer(annotationTableCellRenderer);
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.link.ordinal()).setCellRenderer(linkTableCellRenderer);
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.notes.ordinal()).setCellRenderer(annotationTableCellRenderer);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.species_pattern.ordinal()).setCellRenderer(rbmObservablePatternCellRenderer);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.structure.ordinal()).setCellRenderer(tableRenderer);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.notes.ordinal()).setCellRenderer(annotationTableCellRenderer);
structuresTable.getColumnModel().getColumn(BioModelEditorStructureTableModel.COLUMN_NOTES).setCellRenderer(annotationTableCellRenderer);
// fixed width columns
final int notesWidth = 65;
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setMaxWidth(180);
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.notes.ordinal()).setPreferredWidth(notesWidth);
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.notes.ordinal()).setMaxWidth(notesWidth);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NOTES).setPreferredWidth(notesWidth);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NOTES).setMaxWidth(notesWidth);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.notes.ordinal()).setPreferredWidth(notesWidth);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.notes.ordinal()).setMaxWidth(notesWidth);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEPICTION).setPreferredWidth(180);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_NOTES).setPreferredWidth(notesWidth);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_NOTES).setMaxWidth(notesWidth);
structuresTable.getColumnModel().getColumn(BioModelEditorStructureTableModel.COLUMN_NOTES).setPreferredWidth(notesWidth);
structuresTable.getColumnModel().getColumn(BioModelEditorStructureTableModel.COLUMN_NOTES).setMaxWidth(notesWidth);
// all "depictions" have their own renderer
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setCellRenderer(rbmMolecularTypeShapeDepictionCellRenderer);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_DEPICTION).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_DEFINITION).setCellRenderer(rbmTableRenderer);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.depiction.ordinal()).setCellRenderer(rbmObservableShapeDepictionCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEPICTION).setCellRenderer(rbmReactionShapeDepictionCellRenderer);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.type.ordinal()).setCellEditor(observableTableModel.getObservableTypeComboBoxEditor());
observableTableModel.updateObservableTypeComboBox();
reactionsTable.addMouseListener(eventHandler);
reactionsTable.addKeyListener(eventHandler);
speciesTable.addMouseListener(eventHandler);
speciesTable.addKeyListener(eventHandler);
molecularTypeTable.addMouseListener(eventHandler);
molecularTypeTable.addKeyListener(eventHandler);
observablesTable.addMouseListener(eventHandler);
observablesTable.addKeyListener(eventHandler);
structuresTable.addMouseListener(eventHandler);
structuresTable.addKeyListener(eventHandler);
}
use of cbit.vcell.biomodel.meta.MiriamManager in project vcell by virtualcell.
the class BioModelEditorModelPanel method hasAnnotation.
private boolean hasAnnotation(Identifiable identifiable) {
Identifiable entity = AnnotationsPanel.getIdentifiable(identifiable);
String freeText = bioModel.getVCMetaData().getFreeTextAnnotation(entity);
MiriamManager miriamManager = bioModel.getVCMetaData().getMiriamManager();
TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>> miriamDescrHeir = miriamManager.getMiriamTreeMap();
Map<MiriamRefGroup, MIRIAMQualifier> refGroupMap = miriamDescrHeir.get(entity);
Icon icon = VCellIcons.issueGoodIcon;
if (freeText != null && !freeText.isEmpty()) {
return true;
} else if (refGroupMap != null && !refGroupMap.isEmpty()) {
return true;
}
return false;
}
use of cbit.vcell.biomodel.meta.MiriamManager in project vcell by virtualcell.
the class AnnotationsPanel method removeIdentifier.
private void removeIdentifier() {
Object treeNode = jTreeMIRIAM.getLastSelectedPathComponent();
if (treeNode instanceof LinkNode) {
LinkNode linkNode = (LinkNode) treeNode;
MiriamResource resourceToDelete = linkNode.getMiriamResource();
Identifiable entity = getIdentifiable(selectedObject);
// Map<MiriamRefGroup, MIRIAMQualifier> refGroupsToRemove = vcMetaData.getMiriamManager().getAllMiriamRefGroups(entity);
MiriamManager mm = vcMetaData.getMiriamManager();
Map<MiriamRefGroup, MIRIAMQualifier> refGroupsToRemove = mm.getMiriamTreeMap().get(entity);
boolean found = false;
for (MiriamRefGroup refGroup : refGroupsToRemove.keySet()) {
MIRIAMQualifier qualifier = refGroupsToRemove.get(refGroup);
for (MiriamResource miriamResource : refGroup.getMiriamRefs()) {
if (!isEqual(miriamResource, resourceToDelete)) {
continue;
}
try {
// remove the ref group for this resource
mm.remove2(entity, qualifier, refGroup);
System.out.println(vcMetaData.printRdfStatements());
found = true;
break;
} catch (URNParseFailureException e) {
e.printStackTrace(System.out);
}
}
if (found == true) {
updateInterface();
if (selectedObject instanceof ReactionStep) {
((ReactionStep) selectedObject).firePropertyChange("addIdentifier", true, false);
}
break;
}
}
}
}
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